Applying Large Language Models (LLMs) to heterogeneous enterprise systems is hindered by hallucinations and failures in multi-hop, n-ary reasoning. Existing paradigms (e.g., GraphRAG, NL2SQL) lack the semantic grounding and auditable execution required for these complex environments. We introduce HEAR, an enterprise agentic reasoner built on a Stratified Hypergraph Ontology. Its base Graph Layer virtualizes provenance-aware data interfaces, while the Hyperedge Layer encodes n-ary business rules and procedural protocols. Operating an evidence-driven reasoning loop, HEAR dynamically orchestrates ontology tools for structured multi-hop analysis without requiring LLM retraining. Evaluations on supply-chain tasks, including order fulfillment blockage root cause analysis (RCA), show HEAR achieves up to 94.7% accuracy. Crucially, HEAR demonstrates adaptive efficiency: utilizing procedural hyperedges to minimize token costs, while leveraging topological exploration for rigorous correctness on complex queries. By matching proprietary model performance with open-weight backbones and automating manual diagnostics, HEAR establishes a scalable, auditable foundation for enterprise intelligence.
https://arxiv.org/abs/2605.14259
The literature on ontology-mediated query answering (OMQA) has been shaped by two key results: first-order rewritability for DL-Lite, and PTime-hardness of data complexity for essentially every description logic beyond it. This has effectively positioned DL-Lite as the only practical choice for query rewriting, restricting OMQA solutions to first-order queries and ontologies that can be rewritten into them. This AC0 vs. PTime dichotomy is especially limiting if we consider that OMQA targets graph-structured data, and that standard graph query languages (including the recent ISO standards GQL and SQL/PGQ) are typically NL-complete. Towards identifying a rich Horn DL that can be rewritten into graph query languages and that can still express many ELI and DL-Lite ontologies, we introduce a stratification mechanism for ELI that controls the interaction between conjunction and recursion. In this way, we obtain ELbotpreceq, a description logic that strictly extends the core DL-Lite, supports reachability axioms and restricted conjunction, and allows for reasoning in NL. We establish the NL upper bound via a rewriting into nested two-way regular path queries, a fragment of GQL, providing initial evidence that our ontology language is a promising candidate for extending OMQA to graph query languages.
https://arxiv.org/abs/2605.13367
Do large language models internally encode ontological relations in a formally verifiable algebraic structure? We introduce Algebraic Ontology Projection (AOP), which projects LLM hidden states into the Galois Field F2 under Liskov Substitution Principle constraints, using only 42 relational pairs as algebraic keys. AOP achieves up to 93.33% zero-shot inclusion accuracy on unseen concept pairs (Gemma-2 Instruct with optimized prompt), with consistent 86.67% accuracy observed across multiple model families -- with no model tuning, but through prompt alone. This algebraic structure is strongly layer-dependent. We introduce Semantic Crystallisation (SC), a metric that quantifies F2 constraint satisfaction relative to a random baseline and predicts zero-shot accuracy without held-out data. System prompts act as algebraic boundary conditions: only their combination with instruction tuning prevents Late-layer Collapse -- a systematic degradation of logical consistency in the final layers, observed in 7 of 10 conditions. These findings reframe forward computation as an iterative process of algebraic organisation, and open a path toward LLMs whose logical structure is not merely approximated, but formally accessible.
https://arxiv.org/abs/2605.12968
Evaluating large language models (LLMs) in the biomedical domain requires benchmarks that can distinguish reasoning from pattern matching and remain discriminative as model capabilities improve. Existing biomedical question answering (QA) benchmarks are limited in this respect. Multiple-choice formats can allow models to succeed through answer elimination rather than inference, while widely circulated exam-style datasets are increasingly vulnerable to performance saturation and training data contamination. Multi-hop reasoning, defined as the ability to integrate information across multiple sources to derive an answer, is central to clinically meaningful tasks such as diagnostic support, literature-based discovery, and hypothesis generation, yet remains underrepresented in current biomedical QA benchmarks. MedHopQA is a disease-centered multi-hop reasoning benchmark consisting of 1,000 expert-curated question-answer pairs introduced as a shared task at BioCreative IX. Each question requires synthesis of information across two distinct Wikipedia articles, and answers are provided in an open-ended free-text format. Gold annotations are augmented with ontology-grounded synonym sets from MONDO, NCBI Gene, and NCBI Taxonomy to support both lexical and concept-level evaluation. MedHopQA was constructed through a structured process combining human annotation, triage, iterative verification, and LLM-as-a-judge validation. To reduce leaderboard gaming and contamination risk, the 1,000 scored questions are embedded within a publicly downloadable set of 10,000 questions, with answers withheld, on a CodaBench leaderboard. MedHopQA provides both a benchmark and a reusable framework for constructing future biomedical QA datasets that prioritize compositional reasoning, saturation resistance, and contamination resistance as core design constraints.
https://arxiv.org/abs/2605.12361
Representation learning in electronic health records (EHR) has largely followed paradigms inherited from natural language processing, relying on sequence modeling and reconstruction based objectives that treat clinical labels as ground truth. However, real world clinical supervision is inherently weak, arising from heterogeneous, noisy, and institution specific labeling processes such as billing codes, heuristic phenotypes, and incomplete annotations. In this work, we propose WISTERIA, a weakly supervised representation learning framework that models labels as stochastic observations of an underlying latent clinical state. Instead of optimizing against a single supervision signal, WISTERIA constructs multiple weak supervision operators and learns representations by enforcing consistency across their induced label distributions. This multi view formulation induces an implicit denoising mechanism, allowing the model to recover clinically meaningful structure by reconciling disagreement between noisy labelers. We further incorporate ontology aware regularization in the label space to impose semantic structure over supervision signals. Empirically, WISTERIA improves predictive performance across standard EHR benchmarks, demonstrates strong robustness to label noise, and exhibits superior cross institutional generalization compared to sequence based pretraining objectives. These results suggest that explicitly modeling the supervision process rather than treating labels as fixed targets provides a more appropriate inductive bias for learning robust and clinically meaningful representations from EHR data.
https://arxiv.org/abs/2605.09765
We present Open Ontologies, an open-source ontology engineering system implemented in Rust that integrates LLM-driven construction with formal OWL reasoning and ontology alignment via the Model Context Protocol. Our primary finding is that stable 1-to-1 matching is the dominant factor in ontology alignment quality: on the OAEI Anatomy track, it achieves F1 = 0.832 (P = 0.963, R = 0.733), competitive with state-of-the-art systems and exceeding all in precision. Ablation across five weight configurations shows that signal weights are irrelevant when stable matching is applied (F1 varies by less than 0.004), while removing stable matching drops F1 to 0.728. On the Conference track, the same method achieves F1 = 0.438. On tool-augmented ontology interaction, we find a surprising result: an LLM reading a raw OWL file (F1 = 0.323) performs worse than the same LLM with no file at all (F1 = 0.431), while structured MCP tool access achieves F1 = 0.717. This demonstrates that tool structure provides a qualitatively different mode of access that the LLM cannot replicate by reading raw syntax. The system ships as a single binary under the MIT licence.
https://arxiv.org/abs/2605.09184
Vision--language models (VLMs) show promise for clinical decision support in radiology because they enable joint reasoning over radiological images and clinical text, thereby leveraging complementary clinical information. However, radiological findings are long-tailed in practice, leaving some conditions underrepresented and making zero-shot inference essential. Yet current CLIP-style medical VLMs are sensitive to prompt variations and often lack trustworthy external knowledge at inference time, which hinders reliable clinical deployment. We present \textit{KEPIL}, a prompt-robust framework that integrates curated medical knowledge to stabilize zero-shot generalization. KEPIL comprises: (i) \emph{dynamic prompt enrichment} using ontologies with LLM assistance, (ii) a \emph{semantic-aware contrastive loss} aligning embeddings of equivalent prompt variants via a dual-embedding objective, and (iii) \emph{entity-centric report standardization} to yield ontology-aligned representations. Across seven benchmarks, KEPIL achieves state-of-the-art zero-shot inference performance; under prompt-variation tests, it improves AUC by \(6.37\%\) on \textit{CheXpert} and by \(4.11\%\) on average. These results suggest that structured knowledge and robust prompt design are key to clinically reliable radiology-facing VLMs. Code will be released at this https URL.
https://arxiv.org/abs/2605.09132
Tacit knowledge plays a central role in human expertise, yet it remains difficult to capture, formalize, and reuse in machine-interpretable form. This challenge is especially relevant in procedural domains, where successful execution depends not only on explicit instructions, but also on implicit assumptions, contextual constraints, embodied skills, and experience-based judgments rarely documented. As a result, current knowledge engineering pipelines struggle to transform tacit and process-centric knowledge into formally specified, machine-interpretable representations that can be queried, validated, reasoned over, and reused. In this paper, we introduce a neuro-symbolic framework that combines Logic-Augmented Generation and an Active-Inference-inspired approach for ontology-grounded Knowledge Graph construction. We evaluate the approach in a knowledge transfer case study in manufacturing, using assembly-like repair procedures from instructional videos as a reproducible proxy domain. Results show that the proposed solution improves completeness and semantic quality, advancing neuro-symbolic knowledge engineering for industrial domains.
https://arxiv.org/abs/2605.07639
Evaluating literary quality requires assessing interpretive dimensions such as cultural representation, emotional depth, and philosophical sophistication that resist straightforward computational measurement. We introduce SAGE, a hierarchical evaluation framework that decomposes literary quality into ontology-grounded interpretive dimensions assessed through structured large language model evaluation with multi-round iterative reflection and independent validation. We validate the framework on 100 short stories (50 canonical works, 30 pulp fiction, 20 LLM-generated narratives) across three analytical layers (cultural, emotional-psychological, existential-philosophical) using dual-mode assessment. Across 600 evaluations, the framework achieves 98.8% score convergence and greater than 94% inter-rater agreement, with near-perfect mode invariance between content-based and metadata-based evaluation. Statistical analysis reveals a consistent genre hierarchy (Canonical > Pulp > LLM, all p<0.001) with layer-specific discrimination: cultural critique and philosophical depth exhibit very large effect sizes (Cohen's d>2.4), while emotional representation shows smaller gaps (d=1.68), suggesting that affective patterns are more learnable from training data than critical stance or philosophical depth. Cross-layer correlations (r=0.649-0.683) confirm the three dimensions capture empirically distinguishable quality facets. These findings demonstrate that theory-driven LLM evaluation can achieve measurement-grade reliability and support systematic identification of where current generative models fall short of human literary production, with direct implications for scalable automated evaluation of open-ended text generation.
https://arxiv.org/abs/2605.07102
We present a method for finding hierarchy-aware embeddings of knowledge graphs (KGs) using graph neural networks (GNNs) enriched with a semantic loss derived from underlying ontologies. This method yields embeddings that better reflect domain knowledge. To demonstrate their utility, we predict and interpret the effects of gene deletions in the yeast Saccharomyces cerevisiae and learn box embeddings for KGs in the absence of a prediction task. We further show how box embeddings can serve as the basis for evaluating KG revisions. Our yeast KG is constructed from community databases and ontology terms. Low-dimensional box embeddings combined with GNNs are used to predict cell growth for double gene knockouts. Over 10-fold cross validation, these predictions have a mean $R^2$~score~of~0.360, significantly higher than baseline comparisons, demonstrating that high-level qualitative knowledge is informative about experimental outcomes. Incorporating semantic loss terms in the training of the models improves their predictive performance ($R^2$=0.377) by aligning embeddings with ontology structure. This shows that class hierarchies from ontologies can be exploited for quantitative prediction. We also test the trained models on triple gene knockouts, showing they generalise to data beyond those seen in training. Additionally, by identifying co-occurring relations in the yeast KG important for the cell-growth predictions, we construct hypotheses about interacting traits in yeast. A biological experiment validates one such finding, revealing an association between inositol utilisation and osmotic stress resistance, highlighting the model's potential to guide biological discovery.
https://arxiv.org/abs/2605.03690
The Robotic Service Ontology (RoSO) gives service robotics a typed semantic vocabulary for services, functions, interactions, and deployment-sensitive constraints. Its public revision trail makes visible a harder question than ontology conformance alone can settle: once a service is rebound, recomposed, repaired, or redeployed, under what conditions does the resulting configuration remain an admissible realization of the same protected service? This article argues that the Structural Model of General Intelligence (SMGI) is relevant exactly at that level \citep{osmani2026smgi}. SMGI adds not only a structural interface $\theta$, but an induced behavioral semantics $T_\theta$ and a governance discipline for norm-respecting change. We show that RoSO can be embedded into SMGI as a typed semantic layer, so that service descriptions become dynamically governable rather than merely well formed. This yields a RoSO-to-SMGI adequacy theorem, identity-preserving reconfiguration criteria, and compositional conditions under which locally acceptable updates remain globally admissible. The resulting claim is not that SMGI replaces RoSO, but that it provides a formal account of what admissible runtime change requires once service semantics must survive revision.
https://arxiv.org/abs/2605.08185
The Free Energy Principle (FEP) is a leading framework for mathematically modeling self-organization and learning, while Integrated Information Theory (IIT) is a computational ontology of consciousness oriented around irreducible cause and effect. While conceptual unifications have been proposed and appear to be supported by empirical findings, the absence of a rigorous mathematical mapping places upper bounds on their precision and testability. This work proposes that information can be defined as the deviation $\psi$ of realized dynamics from a constrained maximum-caliber (MaxCal) path ensemble over a finite time horizon. Under this definition, each of the cause/effect repertoires central to IIT 3.0 emerge directly from MaxCal variational principles, allowing IIT's phenomenological calculus to be re-derived from constrained entropy-maximization (CMEP). This framework supplies a theoretical bridge to active inference, which is mathematically dual to CMEP under Langevin dynamics, and offers a principled route for extending IIT to new dynamical regimes. When the approach is applied under the Central Limit Theorem (CLT) for Markov chains and via large deviations theory (LDT) to Ising models, information $\psi$ is shown to be equivalent to prediction error under accompanying predictive coding models. This may hold relevance to the ``hill-shaped trajectory'' of $\Phi$ observed in neuronal cultures adapting to sensory inputs. Together, these results provide a physically and mathematically grounded rationale for studying the convergence of FEP, IIT, and thermodynamic frameworks of cognition such as recent work grounding consciousness in violations of the Fluctuation-Dissipation Theorem (FDT).
https://arxiv.org/abs/2605.12536
Clinical AI adoption is hindered by the black-box/grey-box nature of high-performing models, which lack the ontological grounding and narrative transparency required for professional-level explainability. We present NEURON, a neuro-symbolic system designed to enhance both predictive reliability and clinical interpretability. NEURON integrates SNOMED CT ontology-informed structural representations with machine learning models to bridge the gap between raw data and medical nomenclature. To facilitate human-aligned interaction, the system utilizes a Retrieval-Augmented Generation (RAG) grounded LLM layer to synthesize SHAP feature attributions and patient-specific clinical notes into coherent, natural-language explanations. Validated on the MIMIC-IV dataset for Acute Heart Failure mortality prediction, NEURON improved the AUC from 0.74-0.77 to 0.84-0.88 and significantly outperformed raw SHAP visualizations in human-aligned metrics (0.85 vs. 0.50). Our results demonstrate that NEURON offers a robust, scalable engineering solution for deploying trustworthy, human-centered connected health applications.
https://arxiv.org/abs/2605.01189
This work presents a knowledge-driven decision-support system that integrates structured defect knowledge with LLM-based reasoning to provide explainable defect diagnosis and mitigation guidance in manufacturing, using LPBF as a representative, safety-critical case study. The proposed ontology-integrated LLM-based decision support system for LPBF defect analysis and mitigation guidance is built on a knowledge base containing 27 known LPBF defect types organized into hierarchical categories and causal relationships. The developed system supports fuzzy natural language queries for systematic knowledge retrieval, literature-supported explanation of defects, and guidance on defect causes and mitigation strategies derived from encoded process knowledge. Furthermore, a multimodal image-assessment module based on foundation models enables descriptor-guided interpretation of representative microscopic defect images through semantic alignment scoring. The proposed framework was evaluated through qualitative comparisons with general-purpose vision-language models, an ablation study, and an inter-rater reliability analysis. Evaluation on the literature-derived dataset showed that the fully integrated configuration outperformed the other three evaluated system configurations, achieving a macro-average F1 score of 0.808. Additionally, inter-rater reliability analysis using Cohen's kappa indicated substantial agreement between the model outputs and the literature-derived reference labels. These findings suggest that ontology-guided knowledge representation can improve the consistency, interpretability, and practical usefulness of LLM-assisted LPBF defect analysis.
https://arxiv.org/abs/2605.01100
In this work, we introduce CellxPert, a scalable multimodal foundation model that unifies single-cell and spatial multi-omics within a common representation space. CellxPert jointly encodes transcriptomic (scRNA-seq), chromatin-accessibility (ATAC-seq), and surface-proteomic (CITE-seq) measurements, while directly incorporating MERFISH and imaging mass-cytometry data as 2D or 3D spatial-visual layers. CellxPert facilitates four key downstream tasks out of the box: (i) cell-type annotation across a broad ontology of 154 largely overlapping identities -- the largest label space addressed to date and a stringent test of fine-grained discrimination, (ii) efficient fine-tuning using Low Rank Adaptation (LoRA), (iii) genome-wide transcriptomic response prediction to in-silico perturbations (ISP), and (iv) seamless multi-omic integration across various assays and platforms. Unlike current single-cell foundation models, which approximate gene perturbations by deleting or reordering tokenized gene expression ranks, CellxPert employs a Metropolis-Hastings sampler whose proposal kernel uses the model's masked conditional distributions to transition to new transcriptomic states conditioned on the perturbed genes. This Markov-chain procedure mitigates out-of-distribution artifacts introduced by abrupt token manipulation and produces trajectories that are biologically interpretable. Evaluations on PBMC68K, Replogle Perturb-seq, Systema, and BMMC benchmarks show that CellxPert surpasses classical and state-of-the-art baselines in cell-type annotation, perturbation response prediction, and multi-omic integration.
https://arxiv.org/abs/2605.00930
The risks posed by AI features are increasing as they are rapidly integrated into software applications. In response, regulations and standards for safe and secure AI have been proposed. In this paper, we present an agentic framework that constructs knowledge graphs (KGs) from AI policy documents and retrieves policy-relevant information to answer questions. We build KGs from three AI risk-related polices under two ontology schemas, and then evaluate five LLMs on 42 policy QA tasks spanning six reasoning types, from entity lookup to cross-policy inference, using both heuristic scoring and an LLM-as-judge. KG augmentation improves scores for all five models, and an open, LLM-discovered schema matches or exceeds the formal ontology.
https://arxiv.org/abs/2604.27713
Intent-based networking promises to revolutionize telecommunications network management by enabling operators to specify high-level goals rather than low-level configurations. The TM Forum Intent Ontology (tio) provides a standardized vocabulary for expressing network intents, yet lacks formal validation mechanisms to ensure intent correctness before its admission. We present tio-shacl, the first comprehensive SHACL (Shapes Constraint Language) validation framework for the TMF Intent Ontology. Our contribution includes 56 node shapes and 69 property shapes across all 15 tio v3.6.0 ontology modules, a reusable constraint library with 25 parameterized SPARQL-based constraint components, and novel validation patterns for recursive logical operators, quantity-based constraints, and cross-expectation relationships. We pursued 100% vocabulary coverage (87 classes, 109 properties, 72 functions), cross-implementation compatibility across three major SHACL engines, and validation accuracy on a corpus of 133 test cases. tio-shacl is publicly available under MIT license at this https URL and enables automated syntactic and semantic validation of network intents, addressing a critical gap in the field.
https://arxiv.org/abs/2604.27359
We study the problem of fitting a description logic (DL) ontology to a given set of positive and negative examples that take the form of an ABox and a Boolean query. While previous work has investigated this problem for the expressive DLs ALC and ALCI, we here focus on the Horn DLs EL and ELI, as well as their extensions with the bottom concept. As the query language, we consider atomic queries (AQs), conjunctive queries (rooted CQs), and unions thereof (rooted UCQs). We provide characterization of the existence of a fitting ontology based on simulations, use them to develop decision procedures, and clarify the exact computational complexity. For AQs, the problem is in PTime for both EL and ELI. For rooted CQs and UCQ, it is Sigma_P^2-complete for EL and ExpTime-complete for ELI. Adding the bottom concept does not change any of these complexities. Interestingly, moving from ALC and ALCI to EL and ELI introduces additional technical challenges rather than simplifying the matter.
https://arxiv.org/abs/2604.26976
Privacy-critical domains require phishing detection systems that satisfy contradictory constraints: near-zero false positives to prevent workflow disruption, transparent explanations for non-expert staff, strict regulatory compliance prohibiting sensitive data exposure to external APIs, and robustness against AI-generated attacks. Existing rule-based systems are brittle to novel campaigns, while LLM-based detectors violate privacy regulations through unredacted data transmission. We introduce CyberCane, a neuro-symbolic framework integrating deterministic symbolic analysis with privacy-preserving retrieval-augmented generation (RAG). Our dual-phase pipeline applies lightweight symbolic rules to email metadata, then escalates borderline cases to semantic classification via RAG with automated sensitive data redaction and retrieval from a phishing-only corpus. We further introduce PhishOnt, an OWL ontology enabling verifiable attack classification through formal reasoning chains. Evaluation on DataPhish2025 (12.3k emails; mixed human/LLM) and Nazario/SpamAssassin demonstrates a 78.6-point recall gain over symbolic-only detection on AI-generated threats, with precision exceeding 98% and FPR as low as 0.16%. Healthcare deployment projects a 542x ROI; tunable operating points support diverse risk tolerances, with open-source implementation at this https URL.
https://arxiv.org/abs/2604.23563
Cross-domain task-oriented dialogue requires reasoning over implicit and explicit feasibility constraints while planning long-horizon, multi-turn actions. Large language models (LLMs) can infer such constraints but are unreliable over long horizons, while Reinforcement learning (RL) optimizes long-horizon behavior yet cannot recover constraints from raw dialogue. Naively coupling LLMs with RL is therefore brittle: unverified or unstructured LLM outputs can corrupt state representations and misguide policy learning. Motivated by this, we propose Verified LLM-Knowledge empowered RL (VLK-RL), a hybrid framework that makes LLM-derived constraint reasoning usable for RL. VLK-RL first elicits candidate constraints with an LLM and then verifies them via a dual-role cross-examination procedure to suppress hallucinations and cross-turn inconsistencies. The verified constraints are mapped into ontology-aligned slot-value representations, yielding a structured, constraint-aware state for RL policy optimization. Experiments across multiple benchmarks demonstrate that VLK-RL significantly improves generalization and robustness, outperforming strong single-model baselines on long-horizon tasks.
https://arxiv.org/abs/2604.23345